ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. You can fins more information on abyss [[http://​www.bcgsc.ca/​platform/​bioinfo/​software/​abyss|here]].

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====Environment Setup====

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To work with abyss first we need to load abyss and it's dependencies. The easiest way to do this is to modify the ''​.bashrc''​ file in your ''​$HOME''​ directory.

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<​code>​

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module load gcc

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module load mpi

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module load openmpi

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module load intel/​13.1.0

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module load abyss/2.0.2

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</​code>​

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Create a directory in your ''​$HOME''​ directory where you can submit and run the example job. Copy the ''​fastaq''​ files used for the example job from the examples directory located with the abyss software.